rs5755495

Positions:

• chr22-35002849-C-G
• chr22-35002849-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668433.1(LINC02885):​n.14G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,872 control chromosomes in the GnomAD database, including 29,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (29309 hom., cov: 31)
  • Exomes 𝑓: 0.55 (2 hom.)
• Consequence: LINC02885 ENST00000668433.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

LINC02885 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35002849C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.14G>C		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93241 AN: 151730 Hom.: 29274 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.601

GnomAD4 exome AF: 0.545 AC: 12 AN: 22 Hom.: 2 Cov.: 0 AF XY: 0.550 AC XY: 11 AN XY: 20

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.615 AC: 93335 AN: 151850 Hom.: 29309 Cov.: 31 AF XY: 0.619 AC XY: 45918 AN XY: 74204

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.606

Alfa AF: 0.591 Hom.: 3329

Bravo AF: 0.617

Asia WGS AF: 0.743 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5755495; hg19: chr22-35398839;